Mercurial > repos > vipints > fml_mergeloci
comparison fml_gff_groomer/README @ 0:79726c328621 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | vipints |
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| date | Tue, 07 Jun 2011 17:29:24 -0400 |
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| -1:000000000000 | 0:79726c328621 |
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| 1 A set of tools for pre-processing genome annotation in Generic Feature Format (GFF) | |
| 2 | |
| 3 INTRODUCTION | |
| 4 | |
| 5 Here I am distributing a customized bio-python scripts to give details about the GFF file | |
| 6 before you proceed with any analysis work. This programs allow you to get a better understanding | |
| 7 about your GFF file and do necessary grooming procedure to make them valid for better use. | |
| 8 Please follow the instructions below to clone these tools into your galaxy instance. | |
| 9 | |
| 10 CONTENTS | |
| 11 | |
| 12 galaxy: Contains tool configuration files in *.xml format. | |
| 13 | |
| 14 Tool configuration files. Please add right path to locate the scripts. | |
| 15 | |
| 16 gff_id_mapper.xml | |
| 17 | |
| 18 gff_available_limits.xml | |
| 19 | |
| 20 gff_loci_merge.xml | |
| 21 | |
| 22 | |
| 23 t: Test data set. (move to your galaxy root folder/test-data/) | |
| 24 | |
| 25 You may need to move the test files into your test-data directory so galaxy can find them. | |
| 26 If you want to run the functional tests eg as: | |
| 27 | |
| 28 sh run_functional_tests.sh -id fml_mergeloci | |
| 29 | |
| 30 scripts: Python based and Perl based scripts. | |
| 31 | |
| 32 gff_id_mapper.py : Provides feature to sub feature identifier mapping in a given GFF3 file () | |
| 33 | |
| 34 gff_available_limits.py : This tool provides an overview of available contig identifiers, sources and feature types and their corresponding counts from a given GFF file. | |
| 35 | |
| 36 gff_loci_merge.py : This tool merge the feature annotation of same loci. MergeLoci will be able to merge several transcripts from single loci to a main feature instead of several features. | |
| 37 | |
| 38 REQUIREMENTS | |
| 39 | |
| 40 Python | |
| 41 | |
| 42 COMMENTS/QUESTIONS | |
| 43 | |
| 44 I can be reached at vipin.ts@tuebingen.mpg.de | |
| 45 | |
| 46 LICENSE | |
| 47 | |
| 48 Copyright (C) 2010 Friedrich Miescher Laboratory of the Max Planck Society | |
| 49 | |
| 50 This program is free software; you can redistribute it and/or modify | |
| 51 it under the terms of the GNU General Public License as published by | |
| 52 the Free Software Foundation; either version 3 of the License, or | |
| 53 (at your option) any later version. | |
| 54 | |
| 55 COURTESY | |
| 56 | |
| 57 To the Galaxy Team. |